Competition between RNA polymerase and DNA polymerase for the DNA template

Reducing background absorbance via a double-lock strategy for detection of alkaline phosphatase and α-fetoprotein

Lowering the background signal for more sensitive analysis of determinands is as important as amplifying the target signal. The photoinduced oxidase of fluorescein has been reported, which can catalyze the oxidization of common substrates in a few minutes. As a metaphor for locks and keys, we designed double locks confining the activity of fluorescein to reduce the background absorbance during colorimetric detection. The first lock inhibits the main activity of fluorescein by phosphating. The second lock almost completely deactivates fluorescein by forming coordination nanoparticles (CNPs) via the self-assembly of cerium chloride and fluorescein diphosphate (FDP). The Ce-FDP CNPs are characterized by scanning electron microscope (SEM), dynamic light scattering (DLS), Fourier transform infrared spectrometer (FTIR), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and energy dispersive spectrum (EDS), which show electrostatic formation and amorphous character in the morphology. Alkaline phosphatase (ALP), the key to release fluorescein, can destroy Ce-FDP CNPs along with decomposing FDP by degrading phosphate groups. Therefore, a novel colorimetric strategy for sensitive detection of ALP is established. The detection of α-fetoprotein (AFP) is further succeeded by labeling AFP antibody with ALP. By dramatically reducing the background absorbance, the detection limits of ALP and AFP are as low as 0.014 mU/mL and 0.023 ng/mL, respectively. This convenient, brief, sensitive assay provides a promising prospect for clinical diagnosis. Graphical abstract.

In vitro transcription by RNA polymerase II in extracts of Xenopus oocytes, eggs, and somatic cells

We describe procedures for preparing extracts of Xenopus oocytes, eggs, and somatic cells that will accurately transcribe class II genes. A variety of viral and Xenopus promoters direct the accurate initiation of transcription by RNA polymerase II in these extracts. Optimal ionic conditions (100-200 mM KCl, 12 mM MgCl2), template concentration (20-40 micrograms/ml), incubation time (30-60 min), and temperature (25 degrees C) for class II gene transcription are described.

Two promoters from the Streptomyces plasmid pIJ101 and their expression in Escherichia coli

An RNA polymerase-binding restriction fragment from the small, high-copy-number Streptomyces plasmid pIJ101 has been shown to have promoter activity in vivo using a promoter-probe vector. The nucleotide sequence of the promoter (the pIJ101B promoter) and the approximate position of the transcription start point as identified by in vitro run-off transcription are presented. Both the pIJ101B promoter and the previously characterised pIJ101A promoter were found to promote transcription in Escherichia coli. The transcription start point in E. coli for the pIJ101A promoter has been determined using high-resolution S1 mapping. Initiation occurs at the same point or within 1 or 2 nucleotides of the transcription start point previously identified in Streptomyces lividans, indicating that the same transcriptional signals are recognised in both genera. The data support the idea that one type of RNA polymerase holoenzyme in Streptomyces recognises a class of promoters similar to the major consensus promoters of E. coli, and that the manner of promoter recognition is similar in both genera.

RNA polymerase-DNA interactions in Streptomyces. In vitro studies of a S. lividans plasmid promoter with S. coelicolor RNA polymerase

DNA fragments of the Streptomyces lividans plasmid pIJ101 have been tested for their ability to bind Streptomyces coelicolor RNA polymerase in vitro or to promote transcription in Streptomyces in vivo. One DNA fragment which does both was shown to encode a transcript which was expressed at low cell-density in cultures of pIJ101-containing cells. The transcript start was located on the DNA sequence of the fragment by nucleotide-primed RNA polymerase binding experiments and by S1 nuclease mapping. The pattern of DNase I protection, the sites of enhanced DNase I cleavage and the DNA sequence of the fragment suggest that the RNA polymerase holoenzyme form, which recognizes this promoter, is similar in its interaction with DNA to the major RNA polymerase of Escherichia coli. Regions showing 3/6 nucleotide homology with each of the -35 and -10 regions of the consensus sequence of E. coli promoters are present in the same positions relative to the transcript start. Symmetrical sequences which may be involved in the regulation of expression of the promoter and a potential polypeptide coding sequence can be identified.

RNA polymerase interactions with the upstream region of the E. coli tyrT promoter

The rate of in vivo transcription from the E. coli tRNA and rRNA promoters depends on both cellular growth rate and aminoacid availability. To investigate the molecular mechanisms involved we determined the extent of interaction of RNA polymerase with the promoter of the tyrT stable RNA gene. We show that the enzyme can protect from DNAase I digestion a region of at least 85 bp of the wild-type tyrT promoter and only approximately 62 bp of the lacUV5 mRNA promoter, the protected region extending on the antisense strand to approximately 65 and 42 bp respectively upstream of the transcription startpoint. A mutant tyrT promoter, tyrTp27, is protected more extensively, RNA polymerase interactions extending to at least approximately -130. We propose that these upstream interactions of RNA polymerase perform two functions; activating initiation by polymerase bound at the primary binding site and increasing the concentration of polymerase in the vicinity of the tyrT promoter, thus allowing a high rate of maximal expression and enabling the promoter to be regulated over a wide range of activity.

The formation of acetylaminofluorene adducts in poly(dC-dG) and poly(dA-dT) on reaction with N-acetoxy-2-acetylaminofluorene and the effect of such modification upon the polymers as templates for DNA polymerases

N-Acetoxy-2-acetylaminofluorene (AcO-AAF) reacts with the alternating DNA-like polynucleotides poly(dC-dG) and poly(dA-dT) in vitro to give adducts of the guanine and adenine bases similar to those reported to be formed in DNA. A previously unobserved guanine adduct was detected in the poly(dC-dG). Using a double-labelled [U-14C-dG, 8-3H-G]-poly(dC-dG) we show that this adduct does not involve the 7- or 8-positions of the guanine. Similarly a thymine adduct of unknown structure was observed in poly(dA-dT). Modification of the polymers with AcO-AAF inhibits their capacity to act as templates for Escherichia coli DNA polymerase I and mammalian DNA polymerase alpha although the binding of the polymerases to the polynucleotides is unaffected. Such modification also leads to an increase in the levels of non-complementary nucleotides incorporated into newly synthesised DNA.